X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=b73fffc5abeafae97ef7cfa54e3fbcd4646ea441;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=4e029846a6aa9394ab774641b5b4a08fac7feebc;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index 4e02984..b73fffc 100644 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,11 +20,15 @@ */ package jalview.bin; +import java.util.Locale; + +import jalview.analysis.AlignmentUtils; import jalview.api.StructureSelectionManagerProvider; import jalview.appletgui.AlignFrame; import jalview.appletgui.AlignViewport; import jalview.appletgui.EmbmenuFrame; import jalview.appletgui.FeatureSettings; +import jalview.appletgui.SplitFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; @@ -35,14 +39,22 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileParse; import jalview.io.IdentifyFile; +import jalview.io.JPredFile; import jalview.io.JnetAnnotationMaker; +import jalview.io.NewickFile; import jalview.javascript.JSFunctionExec; import jalview.javascript.JalviewLiteJsApi; import jalview.javascript.JsCallBack; +import jalview.javascript.MouseOverStructureListener; import jalview.structure.SelectionListener; import jalview.structure.StructureSelectionManager; +import jalview.util.ColorUtils; +import jalview.util.HttpUtils; import jalview.util.MessageManager; import java.applet.Applet; @@ -57,13 +69,15 @@ import java.awt.event.ActionEvent; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.io.BufferedReader; +import java.io.IOException; import java.io.InputStreamReader; import java.net.URL; +import java.util.ArrayList; import java.util.Hashtable; +import java.util.List; import java.util.StringTokenizer; import java.util.Vector; -import netscape.javascript.JSException; import netscape.javascript.JSObject; /** @@ -72,23 +86,28 @@ import netscape.javascript.JSObject; * @author $author$ * @version $Revision: 1.92 $ */ -public class JalviewLite extends Applet implements - StructureSelectionManagerProvider, JalviewLiteJsApi +public class JalviewLite extends Applet + implements StructureSelectionManagerProvider, JalviewLiteJsApi { + private static final String TRUE = "true"; + + private static final String FALSE = "false"; + public StructureSelectionManager getStructureSelectionManager() { return StructureSelectionManager.getStructureSelectionManager(this); } // ///////////////////////////////////////// - // The following public methods maybe called + // The following public methods may be called // externally, eg via javascript in HTML page /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences() */ + @Override public String getSelectedSequences() { return getSelectedSequencesFrom(getDefaultTargetFrame()); @@ -99,6 +118,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String) */ + @Override public String getSelectedSequences(String sep) { return getSelectedSequencesFrom(getDefaultTargetFrame(), sep); @@ -111,6 +131,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui * .AlignFrame) */ + @Override public String getSelectedSequencesFrom(AlignFrame alf) { return getSelectedSequencesFrom(alf, separator); // ""+0x00AC); @@ -123,6 +144,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui * .AlignFrame, java.lang.String) */ + @Override public String getSelectedSequencesFrom(AlignFrame alf, String sep) { StringBuffer result = new StringBuffer(""); @@ -151,6 +173,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String, * java.lang.String, java.lang.String) */ + @Override public void highlight(String sequenceId, String position, String alignedPosition) { @@ -164,6 +187,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String, java.lang.String) */ + @Override public void highlightIn(final AlignFrame alf, final String sequenceId, final String position, final String alignedPosition) { @@ -176,7 +200,7 @@ public class JalviewLite extends Applet implements int apos = -1; try { - apos = new Integer(position).intValue(); + apos = Integer.valueOf(position).intValue(); apos--; } catch (NumberFormatException ex) { @@ -187,7 +211,7 @@ public class JalviewLite extends Applet implements // use vamsas listener to broadcast to all listeners in scope if (alignedPosition != null && (alignedPosition.trim().length() == 0 || alignedPosition - .toLowerCase().indexOf("false") > -1)) + .toLowerCase(Locale.ROOT).indexOf("false") > -1)) { java.awt.EventQueue.invokeLater(new Runnable() { @@ -220,6 +244,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String, * java.lang.String) */ + @Override public void select(String sequenceIds, String columns) { selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator); @@ -231,6 +256,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String, * java.lang.String, java.lang.String) */ + @Override public void select(String sequenceIds, String columns, String sep) { selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep); @@ -242,6 +268,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String) */ + @Override public void selectIn(AlignFrame alf, String sequenceIds, String columns) { selectIn(alf, sequenceIds, columns, separator); @@ -253,6 +280,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String, java.lang.String) */ + @Override public void selectIn(final AlignFrame alf, String sequenceIds, String columns, String sep) { @@ -264,8 +292,9 @@ public class JalviewLite extends Applet implements { if (debug) { - System.err.println("Selecting region using separator string '" - + separator + "'"); + jalview.bin.Console + .errPrintln("Selecting region using separator string '" + + separator + "'"); } } // deparse fields @@ -312,23 +341,23 @@ public class JalviewLite extends Applet implements int from = -1, to = -1; try { - from = new Integer(cl.substring(0, p)).intValue(); + from = Integer.valueOf(cl.substring(0, p)).intValue(); from--; } catch (NumberFormatException ex) { - System.err - .println("ERROR: Couldn't parse first integer in range element column selection string '" + jalview.bin.Console.errPrintln( + "ERROR: Couldn't parse first integer in range element column selection string '" + cl + "' - format is 'from-to'"); return; } try { - to = new Integer(cl.substring(p + 1)).intValue(); + to = Integer.valueOf(cl.substring(p + 1)).intValue(); to--; } catch (NumberFormatException ex) { - System.err - .println("ERROR: Couldn't parse second integer in range element column selection string '" + jalview.bin.Console.errPrintln( + "ERROR: Couldn't parse second integer in range element column selection string '" + cl + "' - format is 'from-to'"); return; } @@ -368,13 +397,13 @@ public class JalviewLite extends Applet implements } if (debug) { - System.err.println("Range '" + cl + "' deparsed as [" + from - + "," + to + "]"); + jalview.bin.Console.errPrintln("Range '" + cl + + "' deparsed as [" + from + "," + to + "]"); } } else { - System.err.println("ERROR: Invalid Range '" + cl + jalview.bin.Console.errPrintln("ERROR: Invalid Range '" + cl + "' deparsed as [" + from + "," + to + "]"); } } @@ -383,19 +412,19 @@ public class JalviewLite extends Applet implements int r = -1; try { - r = new Integer(cl).intValue(); + r = Integer.valueOf(cl).intValue(); r--; } catch (NumberFormatException ex) { - if (cl.toLowerCase().equals("sequence")) + if (cl.toLowerCase(Locale.ROOT).equals("sequence")) { // we are in the dataset sequence's coordinate frame. inseqpos = true; } else { - System.err - .println("ERROR: Couldn't parse integer from point selection element of column selection string '" + jalview.bin.Console.errPrintln( + "ERROR: Couldn't parse integer from point selection element of column selection string '" + cl + "'"); return; } @@ -423,14 +452,15 @@ public class JalviewLite extends Applet implements csel.addElement(r); if (debug) { - System.err.println("Point selection '" + cl + jalview.bin.Console.errPrintln("Point selection '" + cl + "' deparsed as [" + r + "]"); } } else { - System.err.println("ERROR: Invalid Point selection '" + cl - + "' deparsed as [" + r + "]"); + jalview.bin.Console + .errPrintln("ERROR: Invalid Point selection '" + cl + + "' deparsed as [" + r + "]"); } } } @@ -445,15 +475,11 @@ public class JalviewLite extends Applet implements SequenceI rs = sel.getSequenceAt(0); start = rs.findIndex(start); end = rs.findIndex(end); - if (csel != null) + List cs = new ArrayList<>(csel.getSelected()); + csel.clear(); + for (Integer selectedCol : cs) { - Vector cs = csel.getSelected(); - csel.clear(); - for (int csi = 0, csiS = cs.size(); csi < csiS; csi++) - { - csel.addElement(rs.findIndex(((Integer) cs.elementAt(csi)) - .intValue())); - } + csel.addElement(rs.findIndex(selectedCol)); } } sel.setStartRes(start); @@ -463,7 +489,8 @@ public class JalviewLite extends Applet implements @Override public void run() { - alf.select(sel, csel); + alf.select(sel, csel, + alf.getAlignViewport().getAlignment().getHiddenColumns()); } }); } @@ -476,7 +503,9 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang. * String, java.lang.String) */ - public String getSelectedSequencesAsAlignment(String format, String suffix) + @Override + public String getSelectedSequencesAsAlignment(String format, + String suffix) { return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(), format, suffix); @@ -489,26 +518,29 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview * .appletgui.AlignFrame, java.lang.String, java.lang.String) */ + @Override public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix) { try { - boolean seqlimits = suffix.equalsIgnoreCase("true"); + FileFormatI theFormat = FileFormats.getInstance().forName(format); + boolean seqlimits = suffix.equalsIgnoreCase(TRUE); if (alf.viewport.getSelectionGroup() != null) { // JBPNote: getSelectionAsNewSequence behaviour has changed - this // method now returns a full copy of sequence data // TODO consider using getSequenceSelection instead here - String reply = new AppletFormatAdapter().formatSequences(format, + String reply = new AppletFormatAdapter().formatSequences(theFormat, new Alignment(alf.viewport.getSelectionAsNewSequence()), seqlimits); return reply; } - } catch (Exception ex) + } catch (IllegalArgumentException ex) { ex.printStackTrace(); - return "Error retrieving alignment in " + format + " format. "; + return "Error retrieving alignment, possibly invalid format specifier: " + + format; } return ""; } @@ -518,6 +550,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder() */ + @Override public String getAlignmentOrder() { return getAlignmentOrderFrom(getDefaultTargetFrame()); @@ -530,6 +563,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame * ) */ + @Override public String getAlignmentOrderFrom(AlignFrame alf) { return getAlignmentOrderFrom(alf, separator); @@ -542,6 +576,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame * , java.lang.String) */ + @Override public String getAlignmentOrderFrom(AlignFrame alf, String sep) { AlignmentI alorder = alf.getAlignViewport().getAlignment(); @@ -559,6 +594,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String, * java.lang.String) */ + @Override public String orderBy(String order, String undoName) { return orderBy(order, undoName, separator); @@ -570,6 +606,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String, * java.lang.String, java.lang.String) */ + @Override public String orderBy(String order, String undoName, String sep) { return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep); @@ -582,6 +619,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String, java.lang.String) */ + @Override public String orderAlignmentBy(AlignFrame alf, String order, String undoName, String sep) { @@ -630,7 +668,7 @@ public class JalviewLite extends Applet implements final String _undoName = undoName; // TODO: deal with synchronization here: cannot raise any events until after // this has returned. - return alf.sortBy(aorder, _undoName) ? "true" : ""; + return alf.sortBy(aorder, _undoName) ? TRUE : ""; } /* @@ -638,9 +676,10 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String) */ + @Override public String getAlignment(String format) { - return getAlignmentFrom(getDefaultTargetFrame(), format, "true"); + return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE); } /* @@ -650,9 +689,10 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame, * java.lang.String) */ + @Override public String getAlignmentFrom(AlignFrame alf, String format) { - return getAlignmentFrom(alf, format, "true"); + return getAlignmentFrom(alf, format, TRUE); } /* @@ -661,6 +701,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String, * java.lang.String) */ + @Override public String getAlignment(String format, String suffix) { return getAlignmentFrom(getDefaultTargetFrame(), format, suffix); @@ -673,20 +714,23 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String) */ + @Override public String getAlignmentFrom(AlignFrame alf, String format, String suffix) { try { - boolean seqlimits = suffix.equalsIgnoreCase("true"); + boolean seqlimits = suffix.equalsIgnoreCase(TRUE); - String reply = new AppletFormatAdapter().formatSequences(format, + FileFormatI theFormat = FileFormats.getInstance().forName(format); + String reply = new AppletFormatAdapter().formatSequences(theFormat, alf.viewport.getAlignment(), seqlimits); return reply; - } catch (Exception ex) + } catch (IllegalArgumentException ex) { ex.printStackTrace(); - return "Error retrieving alignment in " + format + " format. "; + return "Error retrieving alignment, possibly invalid format specifier: " + + format; } } @@ -695,6 +739,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) */ + @Override public void loadAnnotation(String annotation) { loadAnnotationFrom(getDefaultTargetFrame(), annotation); @@ -707,17 +752,18 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame * , java.lang.String) */ + @Override public void loadAnnotationFrom(AlignFrame alf, String annotation) { - if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport() - .getAlignment(), annotation, AppletFormatAdapter.PASTE)) + if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(), + annotation, DataSourceType.PASTE)) { alf.alignPanel.fontChanged(); alf.alignPanel.setScrollValues(0, 0); } else { - alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE); + alf.parseFeaturesFile(annotation, DataSourceType.PASTE); } } @@ -726,6 +772,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) */ + @Override public void loadFeatures(String features, boolean autoenabledisplay) { loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay); @@ -738,10 +785,11 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame * , java.lang.String) */ + @Override public boolean loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay) { - return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, + return alf.parseFeaturesFile(features, DataSourceType.PASTE, autoenabledisplay); } @@ -750,6 +798,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String) */ + @Override public String getFeatures(String format) { return getFeaturesFrom(getDefaultTargetFrame(), format); @@ -762,6 +811,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame, * java.lang.String) */ + @Override public String getFeaturesFrom(AlignFrame alf, String format) { return alf.outputFeatures(false, format); @@ -772,6 +822,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getAnnotation() */ + @Override public String getAnnotation() { return getAnnotationFrom(getDefaultTargetFrame()); @@ -784,6 +835,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame * ) */ + @Override public String getAnnotationFrom(AlignFrame alf) { return alf.outputAnnotations(false); @@ -794,6 +846,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#newView() */ + @Override public AlignFrame newView() { return newViewFrom(getDefaultTargetFrame()); @@ -804,6 +857,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String) */ + @Override public AlignFrame newView(String name) { return newViewFrom(getDefaultTargetFrame(), name); @@ -814,6 +868,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame) */ + @Override public AlignFrame newViewFrom(AlignFrame alf) { return alf.newView(null); @@ -825,6 +880,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame, * java.lang.String) */ + @Override public AlignFrame newViewFrom(AlignFrame alf, String name) { return alf.newView(name); @@ -836,21 +892,22 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String, * java.lang.String) */ + @Override public AlignFrame loadAlignment(String text, String title) { - Alignment al = null; + AlignmentI al = null; - String format = new IdentifyFile().Identify(text, - AppletFormatAdapter.PASTE); try { - al = new AppletFormatAdapter().readFile(text, - AppletFormatAdapter.PASTE, format); + FileFormatI format = new IdentifyFile().identify(text, + DataSourceType.PASTE); + al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE, + format); if (al.getHeight() > 0) { return new AlignFrame(al, this, title, false); } - } catch (java.io.IOException ex) + } catch (IOException ex) { ex.printStackTrace(); } @@ -862,12 +919,13 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String) */ + @Override public void setMouseoverListener(String listener) { setMouseoverListener(currentAlignFrame, listener); } - private Vector javascriptListeners = new Vector(); + private Vector javascriptListeners = new Vector<>(); /* * (non-Javadoc) @@ -876,6 +934,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame * , java.lang.String) */ + @Override public void setMouseoverListener(AlignFrame af, String listener) { if (listener != null) @@ -883,8 +942,8 @@ public class JalviewLite extends Applet implements listener = listener.trim(); if (listener.length() == 0) { - System.err - .println("jalview Javascript error: Ignoring empty function for mouseover listener."); + jalview.bin.Console.errPrintln( + "jalview Javascript error: Ignoring empty function for mouseover listener."); return; } } @@ -895,11 +954,12 @@ public class JalviewLite extends Applet implements .addStructureViewerListener(mol); if (debug) { - System.err.println("Added a mouseover listener for " - + ((af == null) ? "All frames" : "Just views for " - + af.getAlignViewport().getSequenceSetId())); - System.err.println("There are now " + javascriptListeners.size() - + " listeners in total."); + jalview.bin.Console.errPrintln("Added a mouseover listener for " + + ((af == null) ? "All frames" + : "Just views for " + + af.getAlignViewport().getSequenceSetId())); + jalview.bin.Console.errPrintln("There are now " + + javascriptListeners.size() + " listeners in total."); } } @@ -908,6 +968,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String) */ + @Override public void setSelectionListener(String listener) { setSelectionListener(null, listener); @@ -920,6 +981,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame * , java.lang.String) */ + @Override public void setSelectionListener(AlignFrame af, String listener) { if (listener != null) @@ -927,8 +989,8 @@ public class JalviewLite extends Applet implements listener = listener.trim(); if (listener.length() == 0) { - System.err - .println("jalview Javascript error: Ignoring empty function for selection listener."); + jalview.bin.Console.errPrintln( + "jalview Javascript error: Ignoring empty function for selection listener."); return; } } @@ -939,20 +1001,27 @@ public class JalviewLite extends Applet implements .addSelectionListener(mol); if (debug) { - System.err.println("Added a selection listener for " - + ((af == null) ? "All frames" : "Just views for " - + af.getAlignViewport().getSequenceSetId())); - System.err.println("There are now " + javascriptListeners.size() - + " listeners in total."); + jalview.bin.Console.errPrintln("Added a selection listener for " + + ((af == null) ? "All frames" + : "Just views for " + + af.getAlignViewport().getSequenceSetId())); + jalview.bin.Console.errPrintln("There are now " + + javascriptListeners.size() + " listeners in total."); } } - /* - * (non-Javadoc) - * + /** + * Callable from javascript to register a javascript function to pass events + * to a structure viewer. + * + * @param listener + * the name of a javascript function + * @param modelSet + * a token separated list of PDB file names listened for * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String, - * java.lang.String) + * java.lang.String) */ + @Override public void setStructureListener(String listener, String modelSet) { if (listener != null) @@ -960,22 +1029,23 @@ public class JalviewLite extends Applet implements listener = listener.trim(); if (listener.length() == 0) { - System.err - .println("jalview Javascript error: Ignoring empty function for selection listener."); + jalview.bin.Console.errPrintln( + "jalview Javascript error: Ignoring empty function for selection listener."); return; } } - jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener( - this, listener, separatorListToArray(modelSet)); + MouseOverStructureListener mol = new MouseOverStructureListener(this, + listener, separatorListToArray(modelSet)); javascriptListeners.addElement(mol); StructureSelectionManager.getStructureSelectionManager(this) .addStructureViewerListener(mol); if (debug) { - System.err.println("Added a javascript structure viewer listener '" - + listener + "'"); - System.err.println("There are now " + javascriptListeners.size() - + " listeners in total."); + jalview.bin.Console + .errPrintln("Added a javascript structure viewer listener '" + + listener + "'"); + jalview.bin.Console.errPrintln("There are now " + + javascriptListeners.size() + " listeners in total."); } } @@ -986,6 +1056,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui * .AlignFrame, java.lang.String) */ + @Override public void removeJavascriptListener(AlignFrame af, String listener) { if (listener != null) @@ -1001,9 +1072,8 @@ public class JalviewLite extends Applet implements { Object lstn = javascriptListeners.elementAt(ms); JsCallBack lstner = (JsCallBack) lstn; - if ((af == null || lstner.getAlignFrame() == af) - && (listener == null || lstner.getListenerFunction().equals( - listener))) + if ((af == null || lstner.getAlignFrame() == af) && (listener == null + || lstner.getListenerFunction().equals(listener))) { javascriptListeners.removeElement(lstner); msSize--; @@ -1020,7 +1090,8 @@ public class JalviewLite extends Applet implements rprt = debug; if (debug) { - System.err.println("Removed listener '" + listener + "'"); + jalview.bin.Console + .errPrintln("Removed listener '" + listener + "'"); } } else @@ -1030,20 +1101,22 @@ public class JalviewLite extends Applet implements } if (rprt) { - System.err.println("There are now " + javascriptListeners.size() - + " listeners in total."); + jalview.bin.Console.errPrintln("There are now " + + javascriptListeners.size() + " listeners in total."); } } + @Override public void stop() { - System.err.println("Applet " + getName() + " stop()."); + jalview.bin.Console.errPrintln("Applet " + getName() + " stop()."); tidyUp(); } + @Override public void destroy() { - System.err.println("Applet " + getName() + " destroy()."); + jalview.bin.Console.errPrintln("Applet " + getName() + " destroy()."); tidyUp(); } @@ -1097,8 +1170,9 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String, * java.lang.String, java.lang.String) */ - public void mouseOverStructure(final String pdbResNum, - final String chain, final String pdbfile) + @Override + public void mouseOverStructure(final String pdbResNum, final String chain, + final String pdbfile) { final StructureSelectionManagerProvider me = this; java.awt.EventQueue.invokeLater(new Runnable() @@ -1109,18 +1183,19 @@ public class JalviewLite extends Applet implements try { StructureSelectionManager.getStructureSelectionManager(me) - .mouseOverStructure(new Integer(pdbResNum).intValue(), + .mouseOverStructure(Integer.valueOf(pdbResNum).intValue(), chain, pdbfile); if (debug) { - System.err.println("mouseOver for '" + pdbResNum - + "' in chain '" + chain + "' in structure '" + pdbfile - + "'"); + System.err + .println("mouseOver for '" + pdbResNum + "' in chain '" + + chain + "' in structure '" + pdbfile + "'"); } } catch (NumberFormatException e) { - System.err.println("Ignoring invalid residue number string '" - + pdbResNum + "'"); + jalview.bin.Console + .errPrintln("Ignoring invalid residue number string '" + + pdbResNum + "'"); } } @@ -1134,6 +1209,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String) */ + @Override public void scrollViewToIn(final AlignFrame alf, final String topRow, final String leftHandColumn) { @@ -1144,14 +1220,15 @@ public class JalviewLite extends Applet implements { try { - alf.scrollTo(new Integer(topRow).intValue(), new Integer( - leftHandColumn).intValue()); + alf.scrollTo(Integer.valueOf(topRow).intValue(), + Integer.valueOf(leftHandColumn).intValue()); } catch (Exception ex) { - System.err.println("Couldn't parse integer arguments (topRow='" - + topRow + "' and leftHandColumn='" + leftHandColumn - + "')"); + jalview.bin.Console + .errPrintln("Couldn't parse integer arguments (topRow='" + + topRow + "' and leftHandColumn='" + + leftHandColumn + "')"); ex.printStackTrace(); } } @@ -1176,12 +1253,13 @@ public class JalviewLite extends Applet implements { try { - alf.scrollToRow(new Integer(topRow).intValue()); + alf.scrollToRow(Integer.valueOf(topRow).intValue()); } catch (Exception ex) { - System.err.println("Couldn't parse integer arguments (topRow='" - + topRow + "')"); + jalview.bin.Console + .errPrintln("Couldn't parse integer arguments (topRow='" + + topRow + "')"); ex.printStackTrace(); } @@ -1208,12 +1286,12 @@ public class JalviewLite extends Applet implements { try { - alf.scrollToColumn(new Integer(leftHandColumn).intValue()); + alf.scrollToColumn(Integer.valueOf(leftHandColumn).intValue()); } catch (Exception ex) { - System.err - .println("Couldn't parse integer arguments (leftHandColumn='" + jalview.bin.Console.errPrintln( + "Couldn't parse integer arguments (leftHandColumn='" + leftHandColumn + "')"); ex.printStackTrace(); } @@ -1233,7 +1311,10 @@ public class JalviewLite extends Applet implements String file = "No file"; - Button launcher = new Button("Start Jalview"); + String file2 = null; + + Button launcher = new Button( + MessageManager.getString("label.start_jalview")); /** * The currentAlignFrame is static, it will change if and when the user @@ -1262,14 +1343,14 @@ public class JalviewLite extends Applet implements private boolean alignPdbStructures = false; /** - * use an external structure viewer exclusively (no jmols or MCViews will be + * use an external structure viewer exclusively (no jmols or mc_views will be * opened by JalviewLite itself) */ public boolean useXtrnalSviewer = false; public static boolean debug = false; - static String builddate = null, version = null; + static String builddate = null, version = null, installation = null; private static void initBuildDetails() { @@ -1277,14 +1358,15 @@ public class JalviewLite extends Applet implements { builddate = "unknown"; version = "test"; + installation = "applet"; java.net.URL url = JalviewLite.class .getResource("/.build_properties"); if (url != null) { try { - BufferedReader reader = new BufferedReader(new InputStreamReader( - url.openStream())); + BufferedReader reader = new BufferedReader( + new InputStreamReader(url.openStream())); String line; while ((line = reader.readLine()) != null) { @@ -1296,6 +1378,10 @@ public class JalviewLite extends Applet implements { builddate = line.substring(line.indexOf("=") + 1); } + if (line.indexOf("INSTALLATION") > -1) + { + installation = line.substring(line.indexOf("=") + 1); + } } } catch (Exception ex) { @@ -1311,6 +1397,12 @@ public class JalviewLite extends Applet implements return builddate; } + public static String getInstallation() + { + initBuildDetails(); + return installation; + } + public static String getVersion() { initBuildDetails(); @@ -1322,51 +1414,45 @@ public class JalviewLite extends Applet implements /** * init method for Jalview Applet */ + @Override public void init() { - // remove any handlers that might be hanging around from an earlier instance + debug = TRUE.equalsIgnoreCase(getParameter("debug")); try { if (debug) { - System.err.println("Applet context is '" + jalview.bin.Console.errPrintln("Applet context is '" + getAppletContext().getClass().toString() + "'"); } JSObject scriptObject = JSObject.getWindow(this); if (debug && scriptObject != null) { - System.err.println("Applet has Javascript callback support."); + jalview.bin.Console + .errPrintln("Applet has Javascript callback support."); } } catch (Exception ex) { - System.err - .println("Warning: No JalviewLite javascript callbacks available."); + jalview.bin.Console.errPrintln( + "Warning: No JalviewLite javascript callbacks available."); if (debug) { ex.printStackTrace(); } } - /** - * turn on extra applet debugging - */ - String dbg = getParameter("debug"); - if (dbg != null) - { - debug = dbg.toLowerCase().equals("true"); - } + if (debug) { - - System.err.println("JalviewLite Version " + getVersion()); - System.err.println("Build Date : " + getBuildDate()); - + jalview.bin.Console.errPrintln("JalviewLite Version " + getVersion()); + jalview.bin.Console.errPrintln("Build Date : " + getBuildDate()); + jalview.bin.Console.errPrintln("Installation : " + getInstallation()); } String externalsviewer = getParameter("externalstructureviewer"); if (externalsviewer != null) { - useXtrnalSviewer = externalsviewer.trim().toLowerCase() - .equals("true"); + useXtrnalSviewer = externalsviewer.trim().toLowerCase(Locale.ROOT) + .equals(TRUE); } /** * if true disable the check for jmol @@ -1374,7 +1460,7 @@ public class JalviewLite extends Applet implements String chkforJmol = getParameter("nojmol"); if (chkforJmol != null) { - checkForJmol = !chkforJmol.equals("true"); + checkForJmol = !chkforJmol.equals(TRUE); } /** * get the separator parameter if present @@ -1387,13 +1473,14 @@ public class JalviewLite extends Applet implements separator = sep; if (debug) { - System.err.println("Separator set to '" + separator + "'"); + jalview.bin.Console + .errPrintln("Separator set to '" + separator + "'"); } } else { - throw new Error( - "Invalid separator parameter - must be non-zero length"); + throw new Error(MessageManager + .getString("error.invalid_separator_parameter")); } } int r = 255; @@ -1440,38 +1527,41 @@ public class JalviewLite extends Applet implements file = data.toString(); } } + if (getDefaultParameter("enableSplitFrame", true)) + { + file2 = getParameter("file2"); + } - final JalviewLite jvapplet = this; - if (getParameter("embedded") != null - && getParameter("embedded").equalsIgnoreCase("true")) + embedded = TRUE.equalsIgnoreCase(getParameter("embedded")); + if (embedded) { - // Launch as embedded applet in page - embedded = true; - LoadingThread loader = new LoadingThread(file, jvapplet); + LoadingThread loader = new LoadingThread(file, file2, this); loader.start(); } else if (file != null) { - if (getParameter("showbutton") == null - || !getParameter("showbutton").equalsIgnoreCase("false")) + /* + * Start the applet immediately or show a button to start it + */ + if (FALSE.equalsIgnoreCase(getParameter("showbutton"))) + { + LoadingThread loader = new LoadingThread(file, file2, this); + loader.start(); + } + else { - // Add the JalviewLite 'Button' to the page add(launcher); launcher.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - LoadingThread loader = new LoadingThread(file, jvapplet); + LoadingThread loader = new LoadingThread(file, file2, + JalviewLite.this); loader.start(); } }); } - else - { - // Open jalviewLite immediately. - LoadingThread loader = new LoadingThread(file, jvapplet); - loader.start(); - } } else { @@ -1492,7 +1582,8 @@ public class JalviewLite extends Applet implements { if (tries > 0) { - System.err.println("LiveConnect request thread going to sleep."); + jalview.bin.Console + .errPrintln("LiveConnect request thread going to sleep."); } try { @@ -1503,7 +1594,8 @@ public class JalviewLite extends Applet implements ; if (tries++ > 0) { - System.err.println("LiveConnect request thread woken up."); + jalview.bin.Console + .errPrintln("LiveConnect request thread woken up."); } try { @@ -1512,9 +1604,9 @@ public class JalviewLite extends Applet implements { notFailed = true; } - } catch (JSException jsex) + } catch (Exception jsex) { - System.err.println("Attempt " + tries + jalview.bin.Console.errPrintln("Attempt " + tries + " to access LiveConnect javascript failed."); } } @@ -1547,18 +1639,19 @@ public class JalviewLite extends Applet implements { // do onInit with the JS executor thread new JSFunctionExec(this).executeJavascriptFunction(true, - initjscallback, null, "Calling oninit callback '" - + initjscallback + "'."); + initjscallback, null, + "Calling oninit callback '" + initjscallback + "'."); } catch (Exception e) { - System.err.println("Exception when executing _oninit callback '" - + initjscallback + "'."); + jalview.bin.Console + .errPrintln("Exception when executing _oninit callback '" + + initjscallback + "'."); e.printStackTrace(); } } else { - System.err.println("Not executing _oninit callback '" + jalview.bin.Console.errPrintln("Not executing _oninit callback '" + initjscallback + "' - no scripting allowed."); } } @@ -1586,6 +1679,7 @@ public class JalviewLite extends Applet implements frame.setTitle(title); frame.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent e) { if (frame instanceof AlignFrame) @@ -1610,6 +1704,7 @@ public class JalviewLite extends Applet implements frame.dispose(); } + @Override public void windowActivated(WindowEvent e) { if (frame instanceof AlignFrame) @@ -1617,7 +1712,7 @@ public class JalviewLite extends Applet implements ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame; if (debug) { - System.err.println("Activated window " + frame); + jalview.bin.Console.errPrintln("Activated window " + frame); } } // be good. @@ -1632,7 +1727,7 @@ public class JalviewLite extends Applet implements * * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame == * frame) { currentAlignFrame = null; if (debug) { - * System.err.println("Deactivated window "+frame); } } + * jalview.bin.Console.errPrintln("Deactivated window "+frame); } } * super.windowDeactivated(e); } */ }); @@ -1647,6 +1742,7 @@ public class JalviewLite extends Applet implements * @param g * graphics context */ + @Override public void paint(Graphics g) { if (!fileFound) @@ -1656,8 +1752,8 @@ public class JalviewLite extends Applet implements g.fillRect(0, 0, getSize().width, getSize().height); g.setColor(Color.red); g.drawString( - MessageManager.getString("label.jalview_cannot_open_file"), - 5, 15); + MessageManager.getString("label.jalview_cannot_open_file"), 5, + 15); g.drawString("\"" + file + "\"", 5, 30); } else if (embedded) @@ -1698,6 +1794,7 @@ public class JalviewLite extends Applet implements { private boolean running = false; + @Override public void run() { if (running || checkedForJmol) @@ -1716,8 +1813,8 @@ public class JalviewLite extends Applet implements } if (!jmolAvailable) { - System.out - .println("Jmol not available - Using MCview for structures"); + jalview.bin.Console.outPrintln( + "Jmol not available - Using mc_view for structures"); } } catch (java.lang.ClassNotFoundException ex) { @@ -1728,8 +1825,8 @@ public class JalviewLite extends Applet implements jmolAvailable = false; if (debug) { - System.err - .println("Skipping Jmol check. Will use MCView (probably)"); + jalview.bin.Console.errPrintln( + "Skipping Jmol check. Will use mc_view (probably)"); } } checkedForJmol = true; @@ -1745,29 +1842,21 @@ public class JalviewLite extends Applet implements class LoadingThread extends Thread { /** - * State variable: File source - */ - String file; - - /** * State variable: protocol for access to file source */ - String protocol; + DataSourceType protocol; - /** - * State variable: format of file source - */ - String format; + String _file; // alignment file or URL spec - String _file; + String _file2; // second alignment file or URL spec JalviewLite applet; private void dbgMsg(String msg) { - if (applet.debug) + if (JalviewLite.debug) { - System.err.println(msg); + jalview.bin.Console.errPrintln(msg); } } @@ -1775,35 +1864,82 @@ public class JalviewLite extends Applet implements * update the protocol state variable for accessing the datasource located * by file. * - * @param file + * @param path * @return possibly updated datasource string */ - public String setProtocolState(String file) + public String resolveFileProtocol(String path) { - if (file.startsWith("PASTE")) + /* + * is it paste data? + */ + if (path.startsWith("PASTE")) { - file = file.substring(5); - protocol = AppletFormatAdapter.PASTE; + protocol = DataSourceType.PASTE; + return path.substring(5); } - else if (inArchive(file)) + + /* + * is it a URL? + */ + if (path.indexOf("://") != -1) { - protocol = AppletFormatAdapter.CLASSLOADER; + protocol = DataSourceType.URL; + return path; } - else + + /* + * try relative to document root + */ + URL documentBase = getDocumentBase(); + String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase); + if (HttpUtils.isValidUrl(withDocBase)) + { + if (debug) + { + jalview.bin.Console.errPrintln("Prepended document base '" + + documentBase + "' to make: '" + withDocBase + "'"); + } + protocol = DataSourceType.URL; + return withDocBase; + } + + /* + * try relative to codebase (if different to document base) + */ + URL codeBase = getCodeBase(); + String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path, + codeBase); + if (!withCodeBase.equals(withDocBase) + && HttpUtils.isValidUrl(withCodeBase)) { - file = addProtocol(file); - protocol = AppletFormatAdapter.URL; + protocol = DataSourceType.URL; + if (debug) + { + jalview.bin.Console.errPrintln("Prepended codebase '" + codeBase + + "' to make: '" + withCodeBase + "'"); + } + return withCodeBase; } - dbgMsg("Protocol identified as '" + protocol + "'"); - return file; + + /* + * try locating by classloader; try this last so files in the directory + * are resolved using document base + */ + if (inArchive(path)) + { + protocol = DataSourceType.CLASSLOADER; + } + return path; } - public LoadingThread(String _file, JalviewLite _applet) + public LoadingThread(String file, String file2, JalviewLite _applet) { - this._file = _file; + this._file = file; + this._file2 = file2; applet = _applet; } + @Override public void run() { LoadJmolThread jmolchecker = new LoadJmolThread(); @@ -1817,25 +1953,130 @@ public class JalviewLite extends Applet implements } catch (Exception e) { } - ; } startLoading(); // applet.callInitCallback(); } + /** + * Load the alignment and any related files as specified by applet + * parameters + */ private void startLoading() { - AlignFrame newAlignFrame; - dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile"); - file = setProtocolState(_file); + dbgMsg("Loading thread started with:\n>>file\n" + _file + + ">>endfile"); - format = new jalview.io.IdentifyFile().Identify(file, protocol); - dbgMsg("File identified as '" + format + "'"); dbgMsg("Loading started."); - Alignment al = null; + + AlignFrame newAlignFrame = readAlignment(_file); + AlignFrame newAlignFrame2 = readAlignment(_file2); + if (newAlignFrame != null) + { + addToDisplay(newAlignFrame, newAlignFrame2); + loadTree(newAlignFrame); + + loadScoreFile(newAlignFrame); + + loadFeatures(newAlignFrame); + + loadAnnotations(newAlignFrame); + + loadJnetFile(newAlignFrame); + + loadPdbFiles(newAlignFrame); + } + else + { + fileFound = false; + applet.remove(launcher); + applet.repaint(); + } + callInitCallback(); + } + + /** + * Add an AlignFrame to the display; or if two are provided, a SplitFrame. + * + * @param af + * @param af2 + */ + public void addToDisplay(AlignFrame af, AlignFrame af2) + { + if (af2 != null) + { + AlignmentI al1 = af.viewport.getAlignment(); + AlignmentI al2 = af2.viewport.getAlignment(); + AlignmentI cdna = al1.isNucleotide() ? al1 : al2; + AlignmentI prot = al1.isNucleotide() ? al2 : al1; + if (AlignmentUtils.mapProteinAlignmentToCdna(prot, cdna)) + { + al2.alignAs(al1); + SplitFrame sf = new SplitFrame(af, af2); + sf.addToDisplay(embedded, JalviewLite.this); + return; + } + else + { + String msg = "Could not map any sequence in " + af2.getTitle() + + " as " + + (al1.isNucleotide() ? "protein product" : "cDNA") + + " for " + af.getTitle(); + jalview.bin.Console.errPrintln(msg); + } + } + + af.addToDisplay(embedded); + } + + /** + * Read the alignment file (from URL, text 'paste', or archive by + * classloader). + * + * @return + */ + protected AlignFrame readAlignment(String fileParam) + { + if (fileParam == null) + { + return null; + } + String resolvedFile = resolveFileProtocol(fileParam); + AlignmentI al = null; try { - al = new AppletFormatAdapter().readFile(file, protocol, format); + FileFormatI format = new IdentifyFile().identify(resolvedFile, + protocol); + dbgMsg("File identified as '" + format + "'"); + al = new AppletFormatAdapter().readFile(resolvedFile, protocol, + format); + if ((al != null) && (al.getHeight() > 0)) + { + dbgMsg("Successfully loaded file."); + al.setDataset(null); + AlignFrame newAlignFrame = new AlignFrame(al, applet, + resolvedFile, embedded, false); + newAlignFrame.setTitle(resolvedFile); + if (initialAlignFrame == null) + { + initialAlignFrame = newAlignFrame; + } + // update the focus. + currentAlignFrame = newAlignFrame; + + if (protocol == DataSourceType.PASTE) + { + newAlignFrame.setTitle(MessageManager + .formatMessage("label.sequences_from", new Object[] + { applet.getDocumentBase().toString() })); + } + + newAlignFrame.statusBar.setText(MessageManager.formatMessage( + "label.successfully_loaded_file", new Object[] + { resolvedFile })); + + return newAlignFrame; + } } catch (java.io.IOException ex) { dbgMsg("File load exception."); @@ -1844,9 +2085,9 @@ public class JalviewLite extends Applet implements { try { - FileParse fp = new FileParse(file, protocol); + FileParse fp = new FileParse(resolvedFile, protocol); String ln = null; - dbgMsg(">>>Dumping contents of '" + file + "' " + "(" + dbgMsg(">>>Dumping contents of '" + resolvedFile + "' " + "(" + protocol + ")"); while ((ln = fp.nextLine()) != null) { @@ -1855,417 +2096,401 @@ public class JalviewLite extends Applet implements dbgMsg(">>>Dump finished."); } catch (Exception e) { - System.err - .println("Exception when trying to dump the content of the file parameter."); + jalview.bin.Console.errPrintln( + "Exception when trying to dump the content of the file parameter."); e.printStackTrace(); } } } - if ((al != null) && (al.getHeight() > 0)) - { - dbgMsg("Successfully loaded file."); - newAlignFrame = new AlignFrame(al, applet, file, embedded); - if (initialAlignFrame == null) - { - initialAlignFrame = newAlignFrame; - } - // update the focus. - currentAlignFrame = newAlignFrame; + return null; + } - if (protocol == jalview.io.AppletFormatAdapter.PASTE) - { - newAlignFrame.setTitle(MessageManager.formatMessage( - "label.sequences_from", new String[] - { applet.getDocumentBase().toString() })); - } + /** + * Load PDBFiles if any specified by parameter(s). Returns true if loaded, + * else false. + * + * @param alignFrame + * @return + */ + protected boolean loadPdbFiles(AlignFrame alignFrame) + { + boolean result = false; + /* + * Undocumented for 2.6 - + * related to JAL-434 + */ - newAlignFrame.statusBar.setText(MessageManager.formatMessage( - "label.successfully_loaded_file", new String[] - { file })); + applet.setAlignPdbStructures( + getDefaultParameter("alignpdbfiles", false)); + /* + * + * + * + * + * + */ - String treeFile = applet.getParameter("tree"); - if (treeFile == null) - { - treeFile = applet.getParameter("treeFile"); - } + int pdbFileCount = 0; + // Accumulate pdbs here if they are heading for the same view (if + // alignPdbStructures is true) + Vector pdbs = new Vector(); + // create a lazy matcher if we're asked to + jalview.analysis.SequenceIdMatcher matcher = (applet + .getDefaultParameter("relaxedidmatch", false)) + ? new jalview.analysis.SequenceIdMatcher( + alignFrame.getAlignViewport().getAlignment() + .getSequencesArray()) + : null; - if (treeFile != null) + String param; + do + { + if (pdbFileCount > 0) { - try - { - treeFile = setProtocolState(treeFile); - /* - * if (inArchive(treeFile)) { protocol = - * AppletFormatAdapter.CLASSLOADER; } else { protocol = - * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); } - */ - jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, - protocol); - - fin.parse(); - - if (fin.getTree() != null) - { - newAlignFrame.loadTree(fin, treeFile); - dbgMsg("Successfuly imported tree."); - } - else - { - dbgMsg("Tree parameter did not resolve to a valid tree."); - } - } catch (Exception ex) - { - ex.printStackTrace(); - } + param = applet.getParameter("PDBFILE" + pdbFileCount); } - - /* - * Try to load T-Coffee score file - */ - String sScoreFile = applet.getParameter("scoreFile"); - if (sScoreFile != null && !"".equals(sScoreFile)) + else { - try - { - if (debug) - { - System.err - .println("Attempting to load T-COFFEE score file from the scoreFile parameter"); - } - if (!newAlignFrame.loadScoreFile(sScoreFile)) - { - System.err - .println("Failed to parse T-COFFEE parameter as a valid score file ('" - + sScoreFile + "')"); - } - } catch (Exception e) - { - System.err.printf("Cannot read score file: '%s'. Cause: %s \n", - sScoreFile, e.getMessage()); - } + param = applet.getParameter("PDBFILE"); } - // /////////////////////////// - // modify display of features - // we do this before any features have been loaded, ensuring any hidden - // groups are hidden when features first displayed - // - // hide specific groups - // - String param = applet.getParameter("hidefeaturegroups"); - if (param != null) - { - newAlignFrame.setFeatureGroupState(separatorListToArray(param), - false); - // applet.setFeatureGroupStateOn(newAlignFrame, param, false); - } - // show specific groups - param = applet.getParameter("showfeaturegroups"); - if (param != null) - { - newAlignFrame.setFeatureGroupState(separatorListToArray(param), - true); - // applet.setFeatureGroupStateOn(newAlignFrame, param, true); - } - // and now load features - param = applet.getParameter("features"); if (param != null) { - param = setProtocolState(param); + PDBEntry pdb = new PDBEntry(); - newAlignFrame.parseFeaturesFile(param, protocol); - } + String seqstring; + SequenceI[] seqs = null; + String[] chains = null; - param = applet.getParameter("showFeatureSettings"); - if (param != null && param.equalsIgnoreCase("true")) - { - newAlignFrame.viewport.showSequenceFeatures(true); - new FeatureSettings(newAlignFrame.alignPanel); - } + StringTokenizer st = new StringTokenizer(param, " "); - param = applet.getParameter("annotations"); - if (param != null) - { - param = setProtocolState(param); - - if (new AnnotationFile().readAnnotationFile( - newAlignFrame.viewport.getAlignment(), param, protocol)) - { - newAlignFrame.alignPanel.fontChanged(); - newAlignFrame.alignPanel.setScrollValues(0, 0); - } - else + if (st.countTokens() < 2) { - System.err - .println("Annotations were not added from annotation file '" - + param + "'"); - } - - } + String sequence = applet.getParameter("PDBSEQ"); + if (sequence != null) + { + seqs = new SequenceI[] { matcher == null + ? (Sequence) alignFrame.getAlignViewport() + .getAlignment().findName(sequence) + : matcher.findIdMatch(sequence) }; + } - param = applet.getParameter("jnetfile"); - if (param != null) - { - try - { - param = setProtocolState(param); - jalview.io.JPredFile predictions = new jalview.io.JPredFile( - param, protocol); - JnetAnnotationMaker.add_annotation(predictions, - newAlignFrame.viewport.getAlignment(), 0, false); // false==do - // not - // add - // sequence - // profile - // from - // concise - // output - newAlignFrame.alignPanel.fontChanged(); - newAlignFrame.alignPanel.setScrollValues(0, 0); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - /* - * Undocumented for 2.6 - * - related to JAL-434 - */ - applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles", - false)); - /* - * - * - * - * - * - */ - - int pdbFileCount = 0; - // Accumulate pdbs here if they are heading for the same view (if - // alignPdbStructures is true) - Vector pdbs = new Vector(); - // create a lazy matcher if we're asked to - jalview.analysis.SequenceIdMatcher matcher = (applet - .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher( - newAlignFrame.getAlignViewport().getAlignment() - .getSequencesArray()) : null; - - do - { - if (pdbFileCount > 0) - { - param = applet.getParameter("PDBFILE" + pdbFileCount); } else { - param = applet.getParameter("PDBFILE"); - } - - if (param != null) - { - PDBEntry pdb = new PDBEntry(); - - String seqstring; - SequenceI[] seqs = null; - String[] chains = null; - - StringTokenizer st = new StringTokenizer(param, " "); + param = st.nextToken(); + List tmp = new ArrayList<>(); + List tmp2 = new ArrayList<>(); - if (st.countTokens() < 2) + while (st.hasMoreTokens()) { - String sequence = applet.getParameter("PDBSEQ"); - if (sequence != null) - seqs = new SequenceI[] - { matcher == null ? (Sequence) newAlignFrame - .getAlignViewport().getAlignment() - .findName(sequence) : matcher.findIdMatch(sequence) }; - - } - else - { - param = st.nextToken(); - Vector tmp = new Vector(); - Vector tmp2 = new Vector(); - - while (st.hasMoreTokens()) - { - seqstring = st.nextToken(); - StringTokenizer st2 = new StringTokenizer(seqstring, "="); - if (st2.countTokens() > 1) - { - // This is the chain - tmp2.addElement(st2.nextToken()); - seqstring = st2.nextToken(); - } - tmp.addElement(matcher == null ? (Sequence) newAlignFrame - .getAlignViewport().getAlignment() - .findName(seqstring) : matcher - .findIdMatch(seqstring)); - } - - seqs = new SequenceI[tmp.size()]; - tmp.copyInto(seqs); - if (tmp2.size() == tmp.size()) + seqstring = st.nextToken(); + StringTokenizer st2 = new StringTokenizer(seqstring, "="); + if (st2.countTokens() > 1) { - chains = new String[tmp2.size()]; - tmp2.copyInto(chains); + // This is the chain + tmp2.add(st2.nextToken()); + seqstring = st2.nextToken(); } + tmp.add(matcher == null + ? (Sequence) alignFrame.getAlignViewport() + .getAlignment().findName(seqstring) + : matcher.findIdMatch(seqstring)); } - param = setProtocolState(param); - if (// !jmolAvailable - // && - protocol == AppletFormatAdapter.CLASSLOADER - && !useXtrnalSviewer) + seqs = tmp.toArray(new SequenceI[tmp.size()]); + if (tmp2.size() == tmp.size()) { - // Re: JAL-357 : the bug isn't a problem if we are using an - // external viewer! - // TODO: verify this Re: - // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605 - // This exception preserves the current behaviour where, even if - // the local pdb file was identified in the class loader - protocol = AppletFormatAdapter.URL; // this is probably NOT - // CORRECT! - param = addProtocol(param); // + chains = tmp2.toArray(new String[tmp2.size()]); } + } + param = resolveFileProtocol(param); + // TODO check JAL-357 for files in a jar (CLASSLOADER) + pdb.setFile(param); - pdb.setFile(param); - - if (seqs != null) + if (seqs != null) + { + for (int i = 0; i < seqs.length; i++) { - for (int i = 0; i < seqs.length; i++) + if (seqs[i] != null) { - if (seqs[i] != null) - { - ((Sequence) seqs[i]).addPDBId(pdb); - } - else - { - if (JalviewLite.debug) - { - // this may not really be a problem but we give a warning - // anyway - System.err - .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence " - + i + ")"); - } - } - } - - if (!alignPdbStructures) - { - newAlignFrame.newStructureView(applet, pdb, seqs, chains, - protocol); + ((Sequence) seqs[i]).addPDBId(pdb); + StructureSelectionManager + .getStructureSelectionManager(applet) + .registerPDBEntry(pdb); } else { - pdbs.addElement(new Object[] - { pdb, seqs, chains, new String(protocol) }); + if (JalviewLite.debug) + { + // this may not really be a problem but we give a warning + // anyway + jalview.bin.Console.errPrintln( + "Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence " + + i + ")"); + } } } - } - pdbFileCount++; - } while (param != null || pdbFileCount < 10); - if (pdbs.size() > 0) - { - SequenceI[][] seqs = new SequenceI[pdbs.size()][]; - PDBEntry[] pdb = new PDBEntry[pdbs.size()]; - String[][] chains = new String[pdbs.size()][]; - String[] protocols = new String[pdbs.size()]; - for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++) - { - Object[] o = (Object[]) pdbs.elementAt(pdbsi); - pdb[pdbsi] = (PDBEntry) o[0]; - seqs[pdbsi] = (SequenceI[]) o[1]; - chains[pdbsi] = (String[]) o[2]; - protocols[pdbsi] = (String) o[3]; + if (!alignPdbStructures) + { + alignFrame.newStructureView(applet, pdb, seqs, chains, + protocol); + } + else + { + pdbs.addElement(new Object[] { pdb, seqs, chains, protocol }); + } } - newAlignFrame.alignedStructureView(applet, pdb, seqs, chains, - protocols); + } + pdbFileCount++; + } while (param != null || pdbFileCount < 10); + if (pdbs.size() > 0) + { + SequenceI[][] seqs = new SequenceI[pdbs.size()][]; + PDBEntry[] pdb = new PDBEntry[pdbs.size()]; + String[][] chains = new String[pdbs.size()][]; + String[] protocols = new String[pdbs.size()]; + for (int pdbsi = 0, pdbsiSize = pdbs + .size(); pdbsi < pdbsiSize; pdbsi++) + { + Object[] o = (Object[]) pdbs.elementAt(pdbsi); + pdb[pdbsi] = (PDBEntry) o[0]; + seqs[pdbsi] = (SequenceI[]) o[1]; + chains[pdbsi] = (String[]) o[2]; + protocols[pdbsi] = (String) o[3]; } + alignFrame.alignedStructureView(applet, pdb, seqs, chains, + protocols); + result = true; } - else + return result; + } + + /** + * Load in a Jnetfile if specified by parameter. Returns true if loaded, + * else false. + * + * @param alignFrame + * @return + */ + protected boolean loadJnetFile(AlignFrame alignFrame) + { + boolean result = false; + String param = applet.getParameter("jnetfile"); + if (param == null) { - fileFound = false; - applet.remove(launcher); - applet.repaint(); + // jnet became jpred around 2016 + param = applet.getParameter("jpredfile"); } - callInitCallback(); + if (param != null) + { + try + { + param = resolveFileProtocol(param); + JPredFile predictions = new JPredFile(param, protocol); + JnetAnnotationMaker.add_annotation(predictions, + alignFrame.viewport.getAlignment(), 0, false); + // false == do not add sequence profile from concise output + + alignFrame.viewport.getAlignment().setupJPredAlignment(); + + alignFrame.alignPanel.fontChanged(); + alignFrame.alignPanel.setScrollValues(0, 0); + result = true; + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + return result; } /** - * Discovers whether the given file is in the Applet Archive + * Load annotations if specified by parameter. Returns true if loaded, else + * false. * - * @param file - * String - * @return boolean + * @param alignFrame + * @return */ - boolean inArchive(String file) + protected boolean loadAnnotations(AlignFrame alignFrame) { - // This might throw a security exception in certain browsers - // Netscape Communicator for instance. - try + boolean result = false; + String param = applet.getParameter("annotations"); + if (param != null) { - boolean rtn = (getClass().getResourceAsStream("/" + file) != null); - if (debug) + param = resolveFileProtocol(param); + + if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport, + param, protocol)) { - System.err.println("Resource '" + file + "' was " - + (rtn ? "" : "not") + " located by classloader."); + alignFrame.alignPanel.fontChanged(); + alignFrame.alignPanel.setScrollValues(0, 0); + result = true; } - return rtn; - } catch (Exception ex) + else + { + jalview.bin.Console.errPrintln( + "Annotations were not added from annotation file '" + + param + "'"); + } + } + return result; + } + + /** + * Load features file and view settings as specified by parameters. Returns + * true if features were loaded, else false. + * + * @param alignFrame + * @return + */ + protected boolean loadFeatures(AlignFrame alignFrame) + { + boolean result = false; + // /////////////////////////// + // modify display of features + // we do this before any features have been loaded, ensuring any hidden + // groups are hidden when features first displayed + // + // hide specific groups + // + String param = applet.getParameter("hidefeaturegroups"); + if (param != null) { - System.out.println("Exception checking resources: " + file + " " - + ex); - return false; + alignFrame.setFeatureGroupState(separatorListToArray(param), false); + // applet.setFeatureGroupStateOn(newAlignFrame, param, false); + } + // show specific groups + param = applet.getParameter("showfeaturegroups"); + if (param != null) + { + alignFrame.setFeatureGroupState(separatorListToArray(param), true); + // applet.setFeatureGroupStateOn(newAlignFrame, param, true); + } + // and now load features + param = applet.getParameter("features"); + if (param != null) + { + param = resolveFileProtocol(param); + + result = alignFrame.parseFeaturesFile(param, protocol); + } + + param = applet.getParameter("showFeatureSettings"); + if (param != null && param.equalsIgnoreCase(TRUE)) + { + alignFrame.viewport.setShowSequenceFeatures(true); + new FeatureSettings(alignFrame.alignPanel); } + return result; } - String addProtocol(String file) + /** + * Load a score file if specified by parameter. Returns true if file was + * loaded, else false. + * + * @param alignFrame + */ + protected boolean loadScoreFile(AlignFrame alignFrame) { - if (file.indexOf("://") == -1) + boolean result = false; + String sScoreFile = applet.getParameter("scoreFile"); + if (sScoreFile != null && !"".equals(sScoreFile)) { - String fl = applet.resolveUrlForLocalOrAbsolute(file, - getDocumentBase()); try { - if (new java.net.URL(fl).openStream() != null) + if (debug) { - if (debug) - { - System.err.println("Prepended document base for resource: '" - + file + "'"); - } - return fl; + jalview.bin.Console.errPrintln( + "Attempting to load T-COFFEE score file from the scoreFile parameter"); + } + result = alignFrame.loadScoreFile(sScoreFile); + if (!result) + { + jalview.bin.Console.errPrintln( + "Failed to parse T-COFFEE parameter as a valid score file ('" + + sScoreFile + "')"); } - } catch (Exception x) + } catch (Exception e) { + System.err.printf("Cannot read score file: '%s'. Cause: %s \n", + sScoreFile, e.getMessage()); } - ; - fl = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase()); + } + return result; + } + + /** + * Load a tree for the alignment if specified by parameter. Returns true if + * a tree was loaded, else false. + * + * @param alignFrame + * @return + */ + protected boolean loadTree(AlignFrame alignFrame) + { + boolean result = false; + String treeFile = applet.getParameter("tree"); + if (treeFile == null) + { + treeFile = applet.getParameter("treeFile"); + } + + if (treeFile != null) + { try { - if (new java.net.URL(fl).openStream() != null) + treeFile = resolveFileProtocol(treeFile); + NewickFile fin = new NewickFile(treeFile, protocol); + fin.parse(); + + if (fin.getTree() != null) { - if (debug) - { - System.err.println("Prepended codebase for resource: '" - + file + "'"); - } - return fl; + alignFrame.loadTree(fin, treeFile); + result = true; + dbgMsg("Successfully imported tree."); } - } catch (Exception x) + else + { + dbgMsg("Tree parameter did not resolve to a valid tree."); + } + } catch (Exception ex) { + ex.printStackTrace(); } - ; - } + return result; + } - return file; + /** + * Discovers whether the given file is in the Applet Archive + * + * @param f + * String + * @return boolean + */ + boolean inArchive(String f) + { + // This might throw a security exception in certain browsers + // Netscape Communicator for instance. + try + { + boolean rtn = (getClass().getResourceAsStream("/" + f) != null); + if (debug) + { + jalview.bin.Console.errPrintln("Resource '" + f + "' was " + + (rtn ? "" : "not ") + "located by classloader."); + } + return rtn; + } catch (Exception ex) + { + jalview.bin.Console.outPrintln( + "Exception checking resources: " + f + " " + ex); + return false; + } } } @@ -2284,8 +2509,8 @@ public class JalviewLite extends Applet implements { return initialAlignFrame; } - System.err - .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); + jalview.bin.Console.errPrintln( + "Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); return null; } @@ -2319,12 +2544,14 @@ public class JalviewLite extends Applet implements * @param separator * @return elements separated by separator */ - public String[] separatorListToArray(String list, String separator) + public static String[] separatorListToArray(String list, String separator) { - // note separator local variable intentionally masks object field + // TODO use StringUtils version (slightly different...) int seplen = separator.length(); if (list == null || list.equals("") || list.equals(separator)) + { return null; + } java.util.Vector jv = new Vector(); int cp = 0, pos; while ((pos = list.indexOf(separator, cp)) > cp) @@ -2350,19 +2577,19 @@ public class JalviewLite extends Applet implements jv.removeAllElements(); if (debug) { - System.err.println("Array from '" + separator + jalview.bin.Console.errPrintln("Array from '" + separator + "' separated List:\n" + v.length); for (int i = 0; i < v.length; i++) { - System.err.println("item " + i + " '" + v[i] + "'"); + jalview.bin.Console.errPrintln("item " + i + " '" + v[i] + "'"); } } return v; } if (debug) { - System.err.println("Empty Array from '" + separator - + "' separated List"); + jalview.bin.Console.errPrintln( + "Empty Array from '" + separator + "' separated List"); } return null; } @@ -2385,8 +2612,9 @@ public class JalviewLite extends Applet implements * @param separator * @return concatenated string */ - public String arrayToSeparatorList(String[] list, String separator) + public static String arrayToSeparatorList(String[] list, String separator) { + // TODO use StringUtils version StringBuffer v = new StringBuffer(); if (list != null && list.length > 0) { @@ -2403,16 +2631,16 @@ public class JalviewLite extends Applet implements } if (debug) { - System.err.println("Returning '" + separator - + "' separated List:\n"); - System.err.println(v); + System.err + .println("Returning '" + separator + "' separated List:\n"); + jalview.bin.Console.errPrintln(v); } return v.toString(); } if (debug) { - System.err.println("Returning empty '" + separator - + "' separated List\n"); + jalview.bin.Console.errPrintln( + "Returning empty '" + separator + "' separated List\n"); } return "" + separator; } @@ -2422,10 +2650,11 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups() */ + @Override public String getFeatureGroups() { - String lst = arrayToSeparatorList(getDefaultTargetFrame() - .getFeatureGroups()); + String lst = arrayToSeparatorList( + getDefaultTargetFrame().getFeatureGroups()); return lst; } @@ -2436,6 +2665,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame * ) */ + @Override public String getFeatureGroupsOn(AlignFrame alf) { String lst = arrayToSeparatorList(alf.getFeatureGroups()); @@ -2447,10 +2677,11 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean) */ + @Override public String getFeatureGroupsOfState(boolean visible) { - return arrayToSeparatorList(getDefaultTargetFrame() - .getFeatureGroupsOfState(visible)); + return arrayToSeparatorList( + getDefaultTargetFrame().getFeatureGroupsOfState(visible)); } /* @@ -2460,6 +2691,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui * .AlignFrame, boolean) */ + @Override public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible) { return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible)); @@ -2471,11 +2703,12 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui. * AlignFrame, java.lang.String, boolean) */ + @Override public void setFeatureGroupStateOn(final AlignFrame alf, final String groups, boolean state) { final boolean st = state;// !(state==null || state.equals("") || - // state.toLowerCase().equals("false")); + // state.toLowerCase(Locale.ROOT).equals("false")); java.awt.EventQueue.invokeLater(new Runnable() { @Override @@ -2492,6 +2725,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String, * boolean) */ + @Override public void setFeatureGroupState(String groups, boolean state) { setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state); @@ -2502,6 +2736,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getSeparator() */ + @Override public String getSeparator() { return separator; @@ -2512,6 +2747,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String) */ + @Override public void setSeparator(String separator) { if (separator == null || separator.length() < 1) @@ -2522,7 +2758,8 @@ public class JalviewLite extends Applet implements this.separator = separator; if (debug) { - System.err.println("Default Separator now: '" + separator + "'"); + jalview.bin.Console + .errPrintln("Default Separator now: '" + separator + "'"); } } @@ -2543,7 +2780,7 @@ public class JalviewLite extends Applet implements { return def; } - if (stn.toLowerCase().equals("true")) + if (TRUE.equalsIgnoreCase(stn)) { return true; } @@ -2556,6 +2793,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String, java.lang.String) */ + @Override public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile) { @@ -2572,14 +2810,15 @@ public class JalviewLite extends Applet implements return alignPdbStructures; } + @Override public void start() { // callInitCallback(); } - private Hashtable jshashes = new Hashtable(); + private Hashtable jshashes = new Hashtable<>(); - private Hashtable> jsmessages = new Hashtable>(); + private Hashtable> jsmessages = new Hashtable<>(); public void setJsMessageSet(String messageclass, String viewId, String[] colcommands) @@ -2587,7 +2826,7 @@ public class JalviewLite extends Applet implements Hashtable msgset = jsmessages.get(messageclass); if (msgset == null) { - msgset = new Hashtable(); + msgset = new Hashtable<>(); jsmessages.put(messageclass, msgset); } msgset.put(viewId, colcommands); @@ -2605,6 +2844,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String, * java.lang.String) */ + @Override public String getJsMessage(String messageclass, String viewId) { Hashtable msgset = jsmessages.get(messageclass); @@ -2672,22 +2912,13 @@ public class JalviewLite extends Applet implements { return defcolour; } - Color col = jalview.schemes.ColourSchemeProperty - .getAWTColorFromName(colprop); + Color col = ColorUtils.parseColourString(colprop); if (col == null) { - try - { - col = new jalview.schemes.UserColourScheme(colprop).findColour('A'); - } catch (Exception ex) - { - System.err.println("Couldn't parse '" + colprop - + "' as a colour for " + colparam); - col = null; - } + jalview.bin.Console.errPrintln("Couldn't parse '" + colprop + + "' as a colour for " + colparam); } return (col == null) ? defcolour : col; - } public void openJalviewHelpUrl() @@ -2704,27 +2935,60 @@ public class JalviewLite extends Applet implements * form a complete URL given a path to a resource and a reference location on * the same server * - * @param url + * @param targetPath * - an absolute path on the same server as localref or a document * located relative to localref * @param localref * - a URL on the same server as url * @return a complete URL for the resource located by url */ - private String resolveUrlForLocalOrAbsolute(String url, URL localref) + private String resolveUrlForLocalOrAbsolute(String targetPath, + URL localref) { - String codebase = localref.toString(); - if (url.indexOf("/") == 0) + String resolvedPath = ""; + if (targetPath.startsWith("/")) { - url = codebase.substring(0, codebase.length() - - localref.getFile().length()) - + url; + String codebase = localref.toString(); + String localfile = localref.getFile(); + resolvedPath = codebase.substring(0, + codebase.length() - localfile.length()) + targetPath; + return resolvedPath; + } + + /* + * get URL path and strip off any trailing file e.g. + * www.jalview.org/examples/index.html#applets?a=b is trimmed to + * www.jalview.org/examples/ + */ + String urlPath = localref.toString(); + String directoryPath = urlPath; + int lastSeparator = directoryPath.lastIndexOf("/"); + if (lastSeparator > 0) + { + directoryPath = directoryPath.substring(0, lastSeparator + 1); + } + + if (targetPath.startsWith("/")) + { + /* + * construct absolute URL to a file on the server - this is not allowed? + */ + // String localfile = localref.getFile(); + // resolvedPath = urlPath.substring(0, + // urlPath.length() - localfile.length()) + // + targetPath; + resolvedPath = directoryPath + targetPath.substring(1); } else { - url = localref + url; + resolvedPath = directoryPath + targetPath; + } + if (debug) + { + jalview.bin.Console.errPrintln( + "resolveUrlForLocalOrAbsolute returning " + resolvedPath); } - return url; + return resolvedPath; } /** @@ -2744,24 +3008,22 @@ public class JalviewLite extends Applet implements // form valid URL // Should really use docbase, not codebase. URL prepend; - url = resolveUrlForLocalOrAbsolute( - url, - prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase() - : getCodeBase()); + url = resolveUrlForLocalOrAbsolute(url, + prepend = getDefaultParameter("resolvetocodebase", false) + ? getCodeBase() + : getDocumentBase()); if (debug) { - System.err - .println("Show url (prepended " - + prepend - + " - toggle resolvetocodebase if code/docbase resolution is wrong): " - + url); + jalview.bin.Console.errPrintln("Show url (prepended " + prepend + + " - toggle resolvetocodebase if code/docbase resolution is wrong): " + + url); } } else { if (debug) { - System.err.println("Show url: " + url); + jalview.bin.Console.errPrintln("Show url: " + url); } } if (url.indexOf("javascript:") == 0)